Plots
# plots
for(i in c("detPPV","FP.atFDR05","log10QDiff","TP.atFDR05")){
cat("Score analysis: ", i,"\n\n")
## boxplot
# print(
# ggplot(df, aes(x=prop, y=df[[i]], fill=method)) + geom_boxplot() + ylab(i)
# )
if(i!="TP.atFDR05"){
## density plot: score distribution per permutation
print(
ggplot(df, aes(log10(df[[i]]))) + geom_density(aes(fill=method), alpha=0.9) + facet_wrap(~prop) + xlab(i)
)
## violin plot
if(!i %in% c("FP.atFDR05","log10QDiff")){
print(
ggplot(df, aes(x=prop, y=df[[i]], fill=method)) + geom_violin() + facet_wrap(~method) +
guides(fill=FALSE) + ylab(i) + geom_jitter(shape=16, position=position_jitter(0.2))
)
}
}
## boxplot FP
if(i=="FP.atFDR05"){
print(
ggplot(df, aes(x=method, y=df[[i]], fill=method)) + geom_boxplot() +
guides(fill=FALSE) + ylab(i) + coord_flip() + scale_x_discrete(limits = rev(levels(df$method)))
)
}
## violin plot median
print(
ggplot(df, aes(x=prop, y=df[[i]], fill=method)) + geom_violin(draw_quantiles = 0.5) + facet_wrap(~method) +
guides(fill=FALSE) + ylab(i)
)
## mean curves plot
if(i!="FP.atFDR05"){
print(
ggplot(df, aes(x=as.integer(df$prop), y=df[[i]], color=method)) + geom_smooth(alpha=.1) + scale_x_continuous(labels=unique(props.all)) +
ylab(i) + xlab("prop")
)
}
}
## Score analysis: detPPV




## Score analysis: FP.atFDR05



## Score analysis: log10QDiff



## Score analysis: TP.atFDR05


# FP-TP plot (at FDR .05)
## get average number of FP & TP at FDR .05 for each combination of permutation & method
df.agg <- aggregate(df[,c("FP.atFDR05","TP.atFDR05")], by=df[,c("prop","method")], FUN=mean)
## plot
ggplot(df.agg, aes(x=FP.atFDR05, y=TP.atFDR05, color=method, shape=prop, group=method)) + geom_line() + geom_point(size=3) +
geom_label(data=df.agg %>% filter(prop==50), aes(label=method), position=position_jitter(width=3,height=.03))

scores over the datasets

## $miR.122
## original 20 35 50
## 0.732 0.732 0.732 0.732
##
## $miR.133
## original 20 35 50
## 0.733 0.733 0.733 0.733
##
## $miR.138
## original 20 35 50
## 0.694 0.730 0.700 0.696
##
## $miR.145
## original 20 35 50
## 0.686 0.686 0.686 0.650
##
## $miR.184
## original 20 35 50
## 0.600 0.598 0.600 0.598
##
## $miR.190a
## original 20 35 50
## 0.732 0.732 0.702 0.732
##
## $miR.200b
## original 20 35 50
## 0.752 0.745 0.752 0.739
##
## $miR.216a
## original 20 35 50
## 0.628 0.633 0.612 0.561
##
## $miR.217
## original 20 35 50
## 0.698 0.699 0.696 0.698
##
## $miR.219a
## original 20 35 50
## 0.732 0.732 0.732 0.732
##
## $miR.375
## original 20 35 50
## 0.707 0.707 0.707 0.707
##
## $miR.451a
## original 20 35 50
## 0.687 0.687 0.672 0.709
scores over methods

## $aREAmir
## original 20 35 50
## 0.958 0.958 0.958 0.958
##
## $aREAmir2
## original 20 35 50
## 0.958 0.958 0.958 0.958
##
## $EN.up
## original 20 35 50
## 0.006 0.006 0.006 0.006
##
## $EN.down
## original 20 35 50
## 1 1 1 1
##
## $wEN.up
## original 20 35 50
## 0.005 0.005 0.005 0.005
##
## $wEN.down
## original 20 35 50
## 1 1 1 1
##
## $michael.up
## original 20 35 50
## 0.005 0.005 0.005 0.005
##
## $michael.down
## original 20 35 50
## 1 1 1 1
##
## $MW
## original 20 35 50
## 0.876 0.876 0.876 0.918
##
## $KS
## original 20 35 50
## 0.753 0.753 0.726 0.753
##
## $KS2
## original 20 35 50
## 1.000 1.000 1.000 0.958
##
## $GSEA
## original 20 35 50
## 0.584 0.662 0.551 0.527
##
## $modSites
## original 20 35 50
## 1 1 1 1
##
## $modScore
## original 20 35 50
## 1 1 1 1
##
## $regmir.down
## original 20 35 50
## 0.201 0.179 0.198 0.169
##
## $regmir.up
## original 20 35 50
## 0.009 0.009 0.009 0.009
##
## $regmirb.down
## original 20 35 50
## 1 1 1 1
##
## $regmirb.up
## original 20 35 50
## 0.01 0.01 0.01 0.01
##
## $combFish.1
## original 20 35 50
## 1 1 1 1
##
## $combGeom.1
## original 20 35 50
## 1 1 1 1
##
## $combFish.2
## original 20 35 50
## 1.000 1.000 0.958 0.958
##
## $combGeom.2
## original 20 35 50
## 1.000 1.000 1.000 0.958
TP ratio at FDR 0.05 over methods
## $aREAmir
## original 20 35 50
## 0.917 0.917 0.917 0.917
##
## $aREAmir2
## original 20 35 50
## 0.917 0.917 0.917 0.917
##
## $EN.up
## original 20 35 50
## 0 0 0 0
##
## $EN.down
## original 20 35 50
## 1 1 1 1
##
## $wEN.up
## original 20 35 50
## 0 0 0 0
##
## $wEN.down
## original 20 35 50
## 1 1 1 1
##
## $michael.up
## original 20 35 50
## 0 0 0 0
##
## $michael.down
## original 20 35 50
## 1 1 1 1
##
## $MW
## original 20 35 50
## 1 1 1 1
##
## $KS
## original 20 35 50
## 1 1 1 1
##
## $KS2
## original 20 35 50
## 0.917 0.917 0.917 1.000
##
## $GSEA
## original 20 35 50
## 0.250 0.250 0.333 0.250
##
## $modSites
## original 20 35 50
## 1 1 1 1
##
## $modScore
## original 20 35 50
## 1 1 1 1
##
## $regmir.down
## original 20 35 50
## 0 0 0 0
##
## $regmir.up
## original 20 35 50
## 0 0 0 0
##
## $regmirb.down
## original 20 35 50
## 0.833 0.833 0.833 0.833
##
## $regmirb.up
## original 20 35 50
## 0 0 0 0
##
## $combFish.1
## original 20 35 50
## 1 1 1 1
##
## $combGeom.1
## original 20 35 50
## 1 1 1 1
##
## $combFish.2
## original 20 35 50
## 1 1 1 1
##
## $combGeom.2
## original 20 35 50
## 1 1 1 1